We investigate the stability of noncomposite fractional vortex states in a mesoscopic two-band superconductor within the two-component Ginzburg-Landau model. Our analysis explicitly takes into account the relationship between the model parameters and microscopic material parameters, such as partial density of states, Fermi velocities and elements of the electron-phonon coupling matrix. We have found that states with different phase winding number in each band (L-1 not equal L-2) and fractional flux can exist in many different configurations, including rather unconventional ones where the dominating band carries larger winding number and states where vertical bar L-1 - L-2 vertical bar > 1. We present a detailed analysis of the stability of the observed vortex structures with respect to changing the microscopic parameters, showing that, in the weak coupling case, fractional vortex states can be assessed in essentially the whole range of temperatures and applied magnetic fields in which both bands are active. Finally, we propose an efficient way of increasing the range of parameters for which these fractional vortex states can be stabilized. In particular, our proposal allows for observation of fractional vortex structures in materials with stronger coupling, where those states are forbidden at a homogeneous field. This is accomplished with the help of the stray fields of a suitably prepared magnetic dot placed nearby the superconducting disk.